How the Web is Transforming Science

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How the Web is Transforming Science

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devhub-open-science

How the Web is Transforming Science - Talk, for Devmonth by Devhub

On Github acabunoc / devhub-open-science

How the Web is Transforming Science

Devhub, April 2016

Abigail Cabunoc Mayes / @abbycabs

Thank organizers, it's an immense honour to be here. an amazing event! (Amy, Kristen, Andrew, Topaz)

abbycabs.hello();

I work for the Mozilla Foundation where I'm the Lead Developer for the Mozilla Science Lab.

I want to use the web to move science forward.

I work for the science lab *because* I want to use the web & it's power to make things open.

abbycabs.history();

Lead Developer for WormBase, Ontario Institute for Cancer Research

Bioinformatic Research Specialist, Michigan State University

I was working in research labs, and we were dealing with so much data & analysis. It was easy to see how the openness and collaboration available on the web could make science better.

Our mission is to ensure the Internet is a global public resource, open and accessible to all.

Making research collaborative, accessible, and usable.

Science Lab - applying Mozilla's mission to a very interesting community of practice. Where they have some very interesting and specific problems:

Sony PlayStation Portable (PSP) video game graphics

De novo sequence assembly

These both run algorithms that push the limit of the memory that's available to them. 64MB. Jared's story
http://www.thestar.com/news/insight/2015/12/06/gamer-jared-simpson-answers-call-of-duty-to-fight-cancer.html

De novo sequence assembly 101

Image adapted from https://en.wikipedia.org/wiki/Genomic_library#/media/File:Whole_genome_shotgun_sequencing_versus_Hierarchical_shotgun_sequencing.png

open data on the web lets you solve interesting research problems

I wanted to introduce you to some problems I care about, and our community cares about.

Problem 1

Visualizing protein interactions in open worm data to help us understand human diseases.

I wanted to introduce you to some problems I care about, and our community cares about.

Problem 2

Analyzing open genetic data to better understand how virus and bacteria interact.

Problem 3

Collecting and curating open astronomy datasets to facilitate data analysis and discovery.

These problems (& more), are often tackled daily by academics with very little formal computing training. But I think that the people in this room are better equiped to solve these problems -- even without the domain knowledge.

🎉🙌🎉 OPEN SCIENCE 🎉🙌🎉

This talk is really about 'open science'. I know the title is more complex... But I'm really excited to show you how can be a part of this movement, which is really changing how research is done today.

What does 'Open' even mean?

  • open source
  • open access
  • open standards
  • open government
  • open data
  • open science
We've seen this used for... and I think the word 'open' is starting to loose it's meaning When I first heard 'open science' it was vague and I thought it meants something like 'free science'. I want to look back and see how this term came to inspire so many movements and try to bring back some of the meaning & power behind 'open'. And I would argue that a lot of the fundamental ideas behind 'openness' today originates in science!
Welcome to the scientific revolution! Colbert Presenting the Members of the Royal Academy of Sciences to Louis XIV in 1667. At this time, there were a lot of scientific discoveries being made. But people realized they needed a platform to share and collaborate on research.

“Philosophical Transactions of the Royal Society”

Established by the Royal Society of London in 1665

“Philosophical” = “natural philosophy” which is equivalent to “science” today Coming out of the scientific revolution, the first academic journal devoted to science...
Henry OldenburgThe Royal Society’s first secretary, Henry Oldenburg, wrote a series of letters giving us insight into the values driving the creation of the journal.

Credit & Documentation

“We must be very careful as well of regist’ring the person and time of any new matter, as the matter itselfe, whereby the honor of the invention will be reliably preserved to all posterity”24 November 1664

Sharing

“…all ingenious men will thereby be incouraged to impact their knowledge and discoverys ”3 December 1664

Participation

“ … being first revised by some of the members.”Royal Society of London, Council Minutes, 1 March 1665 Need to share discoveries in order to build on them. Science is better with more eyes

Science embraced a culture of working together and sharing discoveries to further human knowledge.

This has enabled many scientific breakthroughs. Today, almost all advances in science appear in a journal article.
WormBase - C. elegans

Fast Forward

The Web + Free Software = New Meaning of 'Open'

some ideas around working open start to appear in the 90s
Essay on the state of free software at the time. Linux
“Linus Torvalds’s style of development—release early and often, delegate everything you can, be open to the point of promiscuity—came as a surprise. No quiet, reverent cathedral-building here—rather, the Linux community seemed to resemble a great babbling bazaar of differing agendas and approaches... out of which a coherent and stable system could seemingly emerge…” Inspired Netscape...

Mozilla

In 1998, the Netscape Corporation released the Netscape browser suite as free software.

This became the basis of the Mozilla Project and inspired the term open source.

https://blog.mozilla.org/beyond-the-code/2012/06/19/two-things-weve-proved-along-the-way/

Working Open

Public and participatory. This requires structuring efforts so that "outsiders" can meaningfully participate and become "insiders" as appropriate.

Working Open, Mozilla Wiki So, how does this look like in open scource?

transparency

→

participation

→

collaboration

"These build on each other" - open source principles Brandon Keepers @bkeepers Open Source Lead at GitHub.

transparency

→

participation

→

collaboration

{

on the web

transparency

→

participation

→

collaboration

software

(understanding software is an onramp to leveraging the web)

Making research collaborative, accessible, and usable

We facilitate learning around open source and data sharing, and empower others to lead in their communities.

Projects we're working with!

and how we're facilitating learning and empowering leaders

Problem 1

Visualizing protein interactions in open worm data to help us understand human diseases.

WormBase & Cytoscape.js

The data (ACeDB)

...

The visualization (Cytoscape.js)

WormBase is the glue that holds the C. elegans research community together. Many in the field start their day with a cup of coffee and WormBase; for many WormBase stays open all day on their computer as a constant companion. There’s simply no more efficient way to integrate all of the new data generated in the field.

Problem 2

Analyzing open genetic data to better understand how virus and bacteria interact.

Problem 3

Collecting and curating open astronomy datasets to facilitate data analysis and discovery.

http://trillianverse.org/

Astronomy produces large data sets from ground-based telescopes, space missions, and simulation. No one institution can host all of this data or properly manage it. Trillian will make it simple and straightforward to apply analyses against full data sets across the wide range of wavelengths available.

Problem 4

Getting credit for your code in academia

Contributorship Badges & Code as a Research Object

Contributorship Badges

Project CRediT: Contributor Roles Taxonomy

  • Conceptualization
  • Data curation
  • Formal analysis
  • Funding acquisition
  • Investigation
  • Methodology
  • Project administration
  • Resources
  • Software
  • Supervision
  • Validation
  • Visualization
  • Writing – original draft
  • Writing – review & editing

The Mozilla Festival 2014

https://github.com/mozillascience/paperbadger

Scientific Software: Credit for your Code

A work in progress. Join us!

+ many more problems like these! These problems (& more), are usually tackled daily by academics with very little formal computing training. But I think that the people in this room are better equiped to solve these problems -- even without the domain knowledge.
Source www.reactiongifs.com

You can help!

Join us at our Global Sprint, June 2-3

Register: http://bit.ly/gs2016to

Acknowledgements

Madeleine Bonsma, Max Franz, Todd Harris, Bill Mills, Demitri Muna, Jared Simpson, Lincoln Stein, Arfon Smith, Matt Jones, Mark Hahnel, Lars Holm Nielsen, Amye Kenall, Laura Paglione, Brian Hole, Austin Davis-Richardson, Ai Deng, Robert Peters, Garth Henson, Anita Perala, Ali Al Dallal, Will Simpson

(+ the Mozilla Science Lab! Kaitlin ThaneyArliss Collins, Zannah Marsh, Aurelia Moser, Steph Wright)

Science is for everyone!

mozillascience.org/volunteer

How the Web is Transforming Science Devhub, April 2016 Abigail Cabunoc Mayes / @abbycabs Thank organizers, it's an immense honour to be here. an amazing event! (Amy, Kristen, Andrew, Topaz)